miRNA: 3'- gGUCCGGUG--------------CCAGGGCGUcGCGC----CAG- -5'
miRNA: 3'- -GGUCCGgUGCCAGGGC-G-----UCG-CGCCAG- -5'
miRNA: 3'- gGUCcGGUGCCagGG-------CGUCGCGCCag -5'
miRNA: 3'- -GGUCCGGUGCCAGGGCGUCGCGCCAG- -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 13624 | 3' | -63.2 | NC_003460.1 | + | 4082 | 0.66 | 0.045703 |
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Target: 5'- aCGGGUCGCgcgccaccccaaggGGUCCCGCGcCGCGucccGUCc -3' miRNA: 3'- gGUCCGGUG--------------CCAGGGCGUcGCGC----CAG- -5' |
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| 13624 | 3' | -63.2 | NC_003460.1 | + | 2009 | 0.66 | 0.044663 |
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Target: 5'- gUCGGGUgAUGGUCCUGgCacguuGGCgGCGGUUa -3' miRNA: 3'- -GGUCCGgUGCCAGGGC-G-----UCG-CGCCAG- -5' |
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| 13624 | 3' | -63.2 | NC_003460.1 | + | 5585 | 0.66 | 0.043076 |
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Target: 5'- gCAGuCCACGGagCCggcugggGCAGCGCGGa- -3' miRNA: 3'- gGUCcGGUGCCagGG-------CGUCGCGCCag -5' |
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| 13624 | 3' | -63.2 | NC_003460.1 | + | 5297 | 1.09 | 5e-06 |
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Target: 5'- gCCAGGCCACGGUCCCGCAGCGCGGUCc -3' miRNA: 3'- -GGUCCGGUGCCAGGGCGUCGCGCCAG- -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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